April 04, 2012

Japanese population substructure (Nishiyama et al. 2012)

PLoS ONE 7(4): e35000. doi:10.1371/journal.pone.0035000

Detailed Analysis of Japanese Population Substructure with a Focus on the Southwest Islands of Japan

Takeshi Nishiyama et al.

Uncovering population structure is important for properly conducting association studies and for examining the demographic history of a population. Here, we examined the Japanese population substructure using data from the Japan Multi-Institutional Collaborative Cohort (J-MICC), which covers all but the northern region of Japan. Using 222 autosomal loci from 4502 subjects, we investigated population substructure by estimating FST among populations, testing population differentiation, and performing principal component analysis (PCA) and correspondence analysis (CA). All analyses revealed a low but significant differentiation between the Amami Islanders and the mainland Japanese population. Furthermore, we examined the genetic differentiation between the mainland population, Amami Islanders and Okinawa Islanders using six loci included in both the Pan-Asian SNP (PASNP) consortium data and the J-MICC data. This analysis revealed that the Amami and Okinawa Islanders were differentiated from the mainland population. In conclusion, we revealed a low but significant level of genetic differentiation between the mainland population and populations in or to the south of the Amami Islands, although genetic variation between both populations might be clinal. Therefore, the possibility of population stratification must be considered when enrolling the islander population of this area, such as in the J-MICC study.

This is a "so what?" paper. There are almost no islands that don't have some differentiation from the adjacent mainland.

But, the paper does nothing to frame the magnitude of the differentiation that they observe relative to the region as a whole. Are these islanders more different from the mainland Japanese than Koreans, than the Chinese, than Japanese individuals from the former region of Ezo in North Japan that is excluded from the study? We aren't told.

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